Phyre 2 and I-Tasser web portal for Protein modeling, Prediction and Validation of gel Q and gel K genes from gellan gum producing bacterial strain Sphingomonas paucimobilis ATCC 31461

Abstract

Gellan gum, an anionic, high-molecular-weight, hetero exo-polysaccharide produced by Sphingomonas paucimobilis ATCC 31461 has potential applications in food and pharmaceutical industries, as a gelling agent, a highly-viscous biogum, a stabilizing agent etc. Three dimensional structure of a protein encoded by a gene could be useful to identify the function of the gene. This study investigates about the 3-D structure prediction of gel Q and gel K protein of Sphingomonas paucimobilis ATCC 31461 using two different protein modeling tools, Phyre2 and I-Tasser. Amplified gel Q and gel K genes were sequenced and the template protein structure identification was carried out using BLASTp with PDB. Superpositioning of the model with the template was analyzed with PyMol. Structure Validation servers of RAMPAGE, PROSA, Verify 3D, ERRAT and Qmean endorsed the 3D structure. The Phyre2 and I-Tasser model of gel Q protein showed best probability conformation with 94.3% and 80.7% residue respectively in the core region of Ramachandran plot showing greater accuracy of model prediction compared to gel K protein with 92.3% and 78.6% residue for Phyre2 and ITasser models respectively. Phyre2 server generated a finer prediction, analysis and validation for gel Q and gel K protein structure than the I-Tasser server. The results generated using Expasy tool also suggested that glycosyl transferase protein, encoded by the genes gel Q and gel K in the gel cluster may be directly involved in the fourth sugar addition of the repeating unit and in the incorporation of GlcA from UDP-glucuronic acid, into glucosyl-α-pyrophosphorylpolyprenol intermediate respectively. In order to develop a recombinant Sphingomonas paucimobilis ATCC 31461, gel Q and gel K gene might be a powerful successor for the overexpression of the gene to enhance gellan gum production.